[Genome] small RNAs, how to check they are intronic and intergenic ?

[Rachel Harte]

Hello James,

You can do this by using the custom track feature and Table Browser tool.
This may be done by creating a custom track for the small RNAs and then do 
two intersections - one with the introns of genes and the other with the 
intergenic regions.

First, to make a custom track, you can easily create a BED format file for 
the small RNAs. Here is the BED file format:

http://genome.ucsc.edu/FAQ/FAQformat#format1

The BED format uses 0-based start coordinates therefore a start of base 1 
is 0 in the BED format so you would need to subtract 1 from the actual 
start positions to create this file.
Then you can upload this BED file to create a custom track. To do this, 
press the button marked "add custom tracks" that is below the Genome Browser 
image or on the Gateway page (follow "Genomes" link on top menu  bar).
Here you can upload your BED file after choosing the appropriate genome 
and assembly.
More information about adding custom tracks can  be found here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html

Once the custom track has been created, you can view it in the Genome 
Browser and it is available in the Table Browser. To reach the Table
Browser, click on the "Tables" link on the top menu bar. Once you have
created a custom track, you can also click on the "go to table browser"
button.

I) To find the small RNAs that are in intronic regions, follow these 
steps. First, create a custom track of intron regions of genes
and then intersect your small RNAs track with the intron regions track.
    1) Select the genome and assembly to which you added your custom track.
    2) Select Genes and Gene Prediction tracks as the group.
    3) Select the gene track that you wish to work with. Known Genes would 
be a good one to pick as a representative gene set. This is not updated as 
frequently as the RefSeq genes but Known Genes includes more mRNA 
transcripts. Note that some mRNAs and RefSeqs may have changed structure 
since the Known Genes track was created.
    4) Select genome as the region and custom track as the output format.
    5) Press get output and select Introns plus 0 bases at each end and 
"get custom track in table browser".
    6) Then select Custom Tracks as the group and select the track and 
table for your small RNAs custom track.
    7) Then press the intersection create button. Select the Custom tracks 
group and select the introns track that you just made. Select the type 
of intersection and press submit. BED is a good choice for output for your
query. This will return a list of small RNAs that overlap with introns.

II) To find small RNAs that are in intergenic regions:
The intersection uses the exons/aligned blocks of the genes. To be able 
to intersect with intergenic regions, you will need to create a custom 
track of the gene footprint i.e. using just the start and end for that 
gene without the exon positions.
To do this, you could use the Table Browser to select just the name, chrom
strand, txStart and txEnd fields for the Known Genes or RefSeq Genes track
using "select fields from primary and related tables" as output format. Then
use the output to create a custom track as you did for the small RNAs. 
Next, you could choose the small RNAs track in the Table Browser and 
intersect it with this custom track of gene positions selecting the option
that finds all the small RNAs that have no overlap with the custom gene 
track. Your output should contain small RNAs that are in the intergenic 
regions.

I hope that this answers your question. Please let us know if you have 
further questions.

Rachel

  >
> ----- Original Message -----
> From: james tan
> To: Genome at soe.ucsc.edu
> Sent: Monday, October 30, 2006 5:00 AM
> Subject: small RNAs, how to check they are intronic and intergenic ?
>
>
> Hi,
>
> I have a set of list of >2000 small RNAs, their start and end coordinates.
> Are there any scripts to check them against the human genome, whether 
> the small RNAs resides in intronic and intergenic regions ?
>
> Thanks
> James
>
>
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-- 
Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu